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Sequence Set Browser

 

AAGH00000000.1 Drosophila simulans

Master
# of Contigs: 31,198
# of Proteins: 15,415
# of Scaffolds: 10,823
Total length: 125,683,891 bp
BioProject: PRJNA12464
BioSample: SAMN02953618
Keywords: WGS
Annotation: Contigs, Scaffolds
Organism: Drosophila simulansshow lineagehide lineage
Biosource:
/mol_type = genomic
/strain = white501
WGS: AAGH01000001:AAGH01031198
Scaffolds: CH447669:CH448480, CH981541:CH984324, CH984325:CH991539, CM000163:CM000168, CM000361:CM000366
10,823 scaffolds, 15,415 proteins, total length is 264,306,695 bases
Reference:
The Genome of Drosophila simulans : Unpublished – Wilson,R.K., The Drosophila simulans Sequencing Consortium
Reference:
Evolution of genes and genomes on the Drosophila phylogeny : Nature 450 (7167), 203-218 (2007) – show 418 authorshide authors
Drosophila 12 Genomes Consortium, Clark,A.G., Eisen,M.B., Smith,D.R., Bergman,C.M., Oliver,B., Markow,T.A., Kaufman,T.C., Kellis,M., Gelbart,W., Iyer,V.N., Pollard,D.A., Sackton,T.B., Larracuente,A.M., Singh,N.D., Abad,J.P., Abt,D.N., Adryan,B., Aguade,M., Akashi,H., Anderson,W.W., Aquadro,C.F., Ardell,D.H., Arguello,R., Artieri,C.G., Barbash,D.A., Barker,D., Barsanti,P., Batterham,P., Batzoglou,S., Begun,D., Bhutkar,A., Blanco,E., Bosak,S.A., Bradley,R.K., Brand,A.D., Brent,M.R., Brooks,A.N., Brown,R.H., Butlin,R.K., Caggese,C., Calvi,B.R., Bernardo de Carvalho,A., Caspi,A., Castrezana,S., Celniker,S.E., Chang,J.L., Chapple,C., Chatterji,S., Chinwalla,A., Civetta,A., Clifton,S.W., Comeron,J.M., Costello,J.C., Coyne,J.A., Daub,J., David,R.G., Delcher,A.L., Delehaunty,K., Do,C.B., Ebling,H., Edwards,K., Eickbush,T., Evans,J.D., Filipski,A., Findeiss,S., Freyhult,E., Fulton,L., Fulton,R., Garcia,A.C., Gardiner,A., Garfield,D.A., Garvin,B.E., Gibson,G., Gilbert,D., Gnerre,S., Godfrey,J., Good,R., Gotea,V., Gravely,B., Greenberg,A.J., Griffiths-Jones,S., Gross,S., Guigo,R., Gustafson,E.A., Haerty,W., Hahn,M.W., Halligan,D.L., Halpern,A.L., Halter,G.M., Han,M.V., Heger,A., Hillier,L., Hinrichs,A.S., Holmes,I., Hoskins,R.A., Hubisz,M.J., Hultmark,D., Huntley,M.A., Jaffe,D.B., Jagadeeshan,S., Jeck,W.R., Johnson,J., Jones,C.D., Jordan,W.C., Karpen,G.H., Kataoka,E., Keightley,P.D., Kheradpour,P., Kirkness,E.F., Koerich,L.B., Kristiansen,K., Kudrna,D., Kulathinal,R.J., Kumar,S., Kwok,R., Lander,E., Langley,C.H., Lapoint,R., Lazzaro,B.P., Lee,S.J., Levesque,L., Li,R., Lin,C.F., Lin,M.F., Lindblad-Toh,K., Llopart,A., Long,M., Low,L., Lozovsky,E., Lu,J., Luo,M., Machado,C.A., Makalowski,W., Marzo,M., Matsuda,M., Matzkin,L., McAllister,B., McBride,C.S., McKernan,B., McKernan,K., Mendez-Lago,M., Minx,P., Mollenhauer,M.U., Montooth,K., Mount,S.M., Mu,X., Myers,E., Negre,B., Newfeld,S., Nielsen,R., Noor,M.A., O'Grady,P., Pachter,L., Papaceit,M., Parisi,M.J., Parisi,M., Parts,L., Pedersen,J.S., Pesole,G., Phillippy,A.M., Ponting,C.P., Pop,M., Porcelli,D., Powell,J.R., Prohaska,S., Pruitt,K., Puig,M., Quesneville,H., Ram,K.R., Rand,D., Rasmussen,M.D., Reed,L.K., Reenan,R., Reily,A., Remington,K.A., Rieger,T.T., Ritchie,M.G., Robin,C., Rogers,Y.H., Rohde,C., Rozas,J., Rubenfield,M.J., Ruiz,A., Russo,S., Salzberg,S.L., Sanchez-Gracia,A., Saranga,D.J., Sato,H., Schaeffer,S.W., Schatz,M.C., Schlenke,T., Schwartz,R., Segarra,C., Singh,R.S., Sirot,L., Sirota,M., Sisneros,N.B., Smith,C.D., Smith,T.F., Spieth,J., Stage,D.E., Stark,A., Stephan,W., Strausberg,R.L., Strempel,S., Sturgill,D., Sutton,G., Sutton,G.G., Tao,W., Teichmann,S., Tobari,Y.N., Tomimura,Y., Tsolas,J.M., Valente,V.L., Venter,E., Venter,J.C., Vicario,S., Vieira,F.G., Vilella,A.J., Villasante,A., Walenz,B., Wang,J., Wasserman,M., Watts,T., Wilson,D., Wilson,R.K., Wing,R.A., Wolfner,M.F., Wong,A., Wong,G.K., Wu,C.I., Wu,G., Yamamoto,D., Yang,H.P., Yang,S.P., Yorke,J.A., Yoshida,K., Zdobnov,E., Zhang,P., Zhang,Y., Zimin,A.V., Baldwin,J., Abdouelleil,A., Abdulkadir,J., Abebe,A., Abera,B., Abreu,J., Acer,S.C., Aftuck,L., Alexander,A., An,P., Anderson,E., Anderson,S., Arachi,H., Azer,M., Bachantsang,P., Barry,A., Bayul,T., Berlin,A., Bessette,D., Bloom,T., Blye,J., Boguslavskiy,L., Bonnet,C., Boukhgalter,B., Bourzgui,I., Brown,A., Cahill,P., Channer,S., Cheshatsang,Y., Chuda,L., Citroen,M., Collymore,A., Cooke,P., Costello,M., D'Aco,K., Daza,R., De Haan,G., DeGray,S., DeMaso,C., Dhargay,N., Dooley,K., Dooley,E., Doricent,M., Dorje,P., Dorjee,K., Dupes,A., Elong,R., Falk,J., Farina,A., Faro,S., Ferguson,D., Fisher,S., Foley,C.D., Franke,A., Friedrich,D., Gadbois,L., Gearin,G., Gearin,C.R., Giannoukos,G., Goode,T., Graham,J., Grandbois,E., Grewal,S., Gyaltsen,K., Hafez,N., Hagos,B., Hall,J., Henson,C., Hollinger,A., Honan,T., Huard,M.D., Hughes,L., Hurhula,B., Husby,M.E., Kamat,A., Kanga,B., Kashin,S., Khazanovich,D., Kisner,P., Lance,K., Lara,M., Lee,W., Lennon,N., Letendre,F., LeVine,R., Lipovsky,A., Liu,X., Liu,J., Liu,S., Lokyitsang,T., Lokyitsang,Y., Lubonja,R., Lui,A., MacDonald,P., Magnisalis,V., Maru,K., Matthews,C., McCusker,W., McDonough,S., Mehta,T., Meldrim,J., Meneus,L., Mihai,O., Mihalev,A., Mihova,T., Mittelman,R., Mlenga,V., Montmayeur,A., Mulrain,L., Navidi,A., Naylor,J., Negash,T., Nguyen,T., Nguyen,N., Nicol,R., Norbu,C., Norbu,N., Novod,N., O'Neill,B., Osman,S., Markiewicz,E., Oyono,O.L., Patti,C., Phunkhang,P., Pierre,F., Priest,M., Raghuraman,S., Rege,F., Reyes,R., Rise,C., Rogov,P., Ross,K., Ryan,E., Settipalli,S., Shea,T., Sherpa,N., Shi,L., Shih,D., Sparrow,T., Spaulding,J., Stalker,J., Stange-Thomann,N., Stavropoulos,S., Stone,C., Strader,C., Tesfaye,S., Thomson,T., Thoulutsang,Y., Thoulutsang,D., Topham,K., Topping,I., Tsamla,T., Vassiliev,H., Vo,A., Wangchuk,T., Wangdi,T., Weiand,M., Wilkinson,J., Wilson,A., Yadav,S., Young,G., Yu,Q., Zembek,L., Zhong,D., Zimmer,A., Zwirko,Z., Jaffe,D.B., Alvarez,P., Brockman,W., Butler,J., Chin,C., Gnerre,S., Grabherr,M., Kleber,M., Mauceli,E., MacCallum,I.
Submission:
Submitted (28-FEB-2005) Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Parkway, St. Louis, MO 63108, USA – Wilson,R.K., The Drosophila simulans Sequencing Consortium
Submission:
Submitted (09-JUN-2008) FlyBase, Harvard University, Biological Laboratories, 16 Divinity Ave., Cambridge, MA 02138, USA – FlyBase

The Drosophila simulans whole genome shotgun (WGS) project has the project accession AAGH00000000. This version of the project (01) has the accession number AAGH01000000, and consists of sequences AAGH01000001-AAGH01031198.

This line is derived from a white501 stock obtained from the Drosophila Species Stock Center in Bowling Green, OH in 1997. It was subsequently inbred by sib-pair mating for nine generations by Daniel Barbash at UC-Davis. The provenance of this line is poorly documented. However, it is likely derived from a Drosophila simulans stock collected in North America in the 1940's. ----- Drosophila simulans Reference Assembly ---- The Drosophila simulans reference assembly is the records CM000361-CM000366 (the chromosomes), CH981541-CH984324 (the random linked, unplaced scaffolds) and CH984325-CH991539 (the unlinked scaffolds). This is the CAF1 assembly of the Drosophila simulans genome. It represents a mosaic of several different D. simulans lines. The assembly process began with a 4x WGS assembly of the D. simulans white501 (w501) line, AAGH00000000. The w501 contigs were initially anchored, ordered and oriented by alignment with the D. melanogaster genome. The assembly was then examined for places where the w501 assembly suggested inversions with respect to the D. melanogaster assembly. One major inversion was found, confirming the already documented inversion found by Lemeunier and Ashburner (1976). Six other D. simulans lines (C167.4, MD106TS, MD199S, New Caledonia 48S, SIM4, and SIM6) were assembled with approximately 1x coverage (WGS projects AASR00000000-AASW00000000, respectively). The 4x WGS assembly of the D. simulans w501 genome was used as a scaffold, and the contigs and unplaced reads from the 1x assemblies of the other individual D. simulans lines were used to cover gaps in the w501 assembly where possible. Thus the resulting assembly is a mosaic containing the w501 contigs as the primary scaffolding, with contigs and unplaced reads from the other lines filling gaps in the w501 assembly. Total size is 142,405,747 bp including gaps and 127,241,461 bp excluding gaps. For more information about the D. simulans assembly and statistics, see the WUSTL Genome Sequencing Center Drosophila simulans web page from the home page, http://genome.wustl.edu/home.cgi. The gene annotation is based on FlyBase Release 1.3, which contains some corrections of the original annotation published by the Drosophila 12 Genomes Consortium. Annotation was added to the scaffolds in July 2008.

Contigs
Download
GenBank:AAGH01.1.gbff.gz 61.9 Mb
FASTA:AAGH01.1.fsa_nt.gz 37.2 Mb
ASN.1:AAGH01.1.bbs.gz 68.5 Mb